Bioinformatik

This book covers recent trends and applications of nonlinear dynamics in various branches of society, science, and engineering. The selected peer-reviewed contributions were presented at the International Conference on Nonlinear Dynamics and Applications (ICNDA 2022) at Sikkim Manipal Institute of Technology (SMIT) and cover a broad swath of topics ranging from chaos theory and fractals to quantum systems and the dynamics of the COVID-19 pandemic. Organized by the SMIT Department of Mathematics, this international conference offers an interdisciplinary stage for scientists, researchers, and inventors to present and discuss the latest innovations and trends in all possible areas of nonlinear dynamics.

Boolean Satisfiability (SAT)is one of the famous problem present in the field of computer scienceand mathematical theory. Boolean Satisfiability can be defined as the problem of finding assignmentsto the variables such that, it satisfy the given a Boolean formula. Boolean Satisfiabilityproblems arise in many applications such as cryptology, hardware and software verification,reliability, artificial intelligence, decision under logic constraints, computational studies of Biologicalnetworks. Recent application of solving Boolean systems arises in Biological(Genetic Regulatory) Networks.The CNF Satisfiability(CNFSAT) Problem is one of the important case of of the SatisfiabilityProblem, where the Boolean formula is represented in the CNF form i.e.Conjunctive NormalForm (CNF).This means Boolean formula is a conjunction of clauses and each clause is a disjunctionof literals. A literal is a variable or its negation.CNF SAT has central importance incomputer science. SAT normally suits to the formulas if they are in Conjunctive NormalForm , as mentioned, should be a set of clauses.SAT is considered as NP-complete problem in its general form. Inspite of this reality,there are number of problems which can be successfully solved by SAT such as cryptanalysis,bioinformatics, hardware verification, etc. For recent past twenty years the effectiveness ofSAT algorithms has significantly increased. XOR-SAT is one special case of Boolean SAT where each equation is an exclusive OR(XOR) combination of variables. Such linear XOR systems naturally appear in problems suchas quadratic sieve method for prime factorization of numbers. Also in decoding of linearerror correction coding, linear XOR systems.In the specific case of cryptography, SAT solversbecame a very important tool to analyse and break encoding mechanisms. Within the case ofcryptanalytic application, many times SAT solvers have faced with issues that encode relativelylarge amount of XOR constraints.

This handbook in two volumes offers a heretofore unavailable compilation of detailed information on foraminifera of the Caspian-Black Sea-Mediterranean Corridors ("e;CORRIDORS"e;), including their taxonomy, ecology, and applications in the study of Quaternary stratigraphy, paleogeographic reconstruction, and environmental stress. This subject is significant in light of the ongoing debates regarding the Flood Hypotheses because foraminifera can provide more information about many of the disputed questions. Foraminifera are highly reliable paleoenvironmental indicators, ubiquitous in marine environments, and taxonomically diverse, which gives them the potential for a wide range of biological responses to varied environmental factors. Their tests are readily preserved and can record evidence of environmental change through time, thus providing historical baseline data even in the absence of background studies. This book presents taxonomic descriptions for about 500 species and subspecies from the Black Sea, Sea of Azov, Caspian Sea, Aral Sea, Sea of Marmara, and the Eastern Mediterranean. This catalogue is supplemented by ecological remarks, stratigraphic distributions, paleogeography, and environmental/paleoenvironmental applications, including responses to environmental stress, e.g., river discharge, pollution by different contaminants, etc. The book will be useful to specialists in Quaternary history of the "e;CORRIDORS"e; as well as those in environmental monitoring and risk assessment. This handbook offers detailed taxonomic descriptions of foraminifera from the Black Sea, Caspian Sea, Sea of Azov, Aral Sea (in Volume 1) and Eastern Mediterranean and Sea of Marmara (in Volume 2). 

This volume provides readers with a broad collection of theoretical, computational, and experimental methods to quantitatively study the properties of phase-separate biomolecular condensates in diverse systems. The chapters in this book cover topics such as theoretical and computational methods; methods for in vitro characterization of biomolecular condensates; and techniques that enable in-cell characterization of biomolecular condensates. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls.Comprehensive and thorough, Phase-Separated Biomolecular Condensates: Methods and Protocols is a valuable resource that helps researchers learn and use established methods to study both biophysical properties and biological functions of biomolecular condensates. 

This volume provides protocols for computational, statistical, and machine learning methods that are mainly applied to the study of metabolic engineering, synthetic biology, and disease applications. These techniques support the latest progress in cross-disciplinary research that integrates the different scales of biological complexity. The topics covered in this book are geared toward researchers with a background in engineering, computational analytical, and modeling experience and cover a broad range of topics in computational and machine learning approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Comprehensive and practical, Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology is a valuable resource for any researcher or scientist who wants to learn more about the latest computational methods and how they are applied toward the understanding and prediction of complex biology. 

Applied Multivariate Statistical Analysis in Medicine provides a multivariate conceptual framework that allows readers to understand the interconnectivity and interrelations among variables, which maintains the intrinsic precision of statistical theories. With a strong focus on the fundamental concepts of multivariate statistical analysis, the book also gives insight into the applications of multivariate distribution in biomedical fields. In 14 chapters, Applied Multivariate Statistical Analysis in Medicine covers the main topics of multivariate analysis methods widely used in health science research. The content is organized progressively from fundamental concepts to sophisticated methods. It begins with basic descriptive statistics in multivariate analysis and follows with parameter estimation, in addition to the hypothesis testing of a multivariate normal distribution, which has heavy applications in biomedical fields where the relationships among approximately normal variables are of great interest. Keeping mathematics to a minimum, considerable emphasis is placed on explanations and real-world applications of core principles to maintain a good balance between introducing theory and cultivating problem-solving skills. This book is a very valuable reference text for clinicians, medical researchers, and other researchers across medical and biomedical disciplines, all of whom confront increasingly complex statistical methods during the analysis and presentation of their results.

This book constitutes the refereed conference proceedings of the 14th International Conference on Bio-inspired Information and Communications Technologies, held in Okinawa, Japan, during April 11-12, 2023. The 17 full papers were carefully reviewed and selected from 33 submissions. The papers focus on the latest research that leverages the understanding of key principles, processes, and mechanisms in biological systems for development of novel information and communications technologies (bio-inspired ICT). BICT 2023 will also highlight innovative research and technologies being developed for biomedicine that are inspired by ICT (ICT-inspired biomedicine).

This contributed volume investigates several mathematical techniques for the modeling and simulation of viral pandemics, with a special focus on COVID-19.  Modeling a pandemic requires an interdisciplinary approach with other fields such as epidemiology, virology, immunology, and biology in general.  Spatial dynamics and interactions are also important features to be considered, and a multiscale framework is needed at the level of individuals and the level of virus particles and the immune system.  Chapters in this volume address these items, as well as offer perspectives for the future.

Dieses Buch umfasst und beschäftigt sich mit den jüngsten Fortschritten und modernsten Anwendungen von naturinspirierten Computertechniken (NIC) im Bereich der Bioinformatik und der Computerbiologie, die die medizinischen Wissenschaften bei verschiedenen klinischen Anwendungen unterstützen können. Dieser Sammelband befasst sich mit den grundlegenden Anwendungen, dem Umfang und den Zukunftsperspektiven von NIC-Techniken in der Bioinformatik, einschließlich der Erstellung von Genomprofilen, der Klassifizierung von Genexpressionsdaten, der DNA-Berechnung, der System- und Netzwerkbiologie, der Lösung von Komplikationen bei personalisierten Therapien, der antimikrobiellen Resistenz bei bakteriellen Krankheitserregern und der computergestützten Entwicklung von Arzneimitteln, deren Entdeckung und Therapie. Darüber hinaus wird die Rolle von NIC-Techniken bei verschiedenen Krankheiten und Störungen behandelt, einschließlich Krebserkennung und -diagnose, Brustkrebs, Erkennung von Lungenkrankheiten, Krankheits-Biomarkern und Identifizierung potenzieller Therapeutika.

This book constitutes the refereed proceedings of the 19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023, held in Wroc¿aw, Poland, during October 9¿12, 2023.The 28 full papers and 16 short papers included in this book were carefully reviewed and selected from 89 submissions. They were organized in topical sections as follows: reconciling inconsistent molecular structures from biochemical databases; radiology report generation via visual recalibration and context gating-aware; sequence-based nanobody-antigen binding prediction; and hist2Vec: kernel-based embeddings for biological sequence classification.

This book focuses on the multi-omics big-data integration, the data-mining techniques and the cutting-edge omics researches in principles and applications for a deep understanding of Traditional Chinese Medicine (TCM) and diseases from the following aspects: (1) Basics about multi-omics data and analytical methods for TCM and diseases. (2) The needs of omics studies in TCM researches, and the basic background of omics research in TCM and disease. (3) Better understanding of the multi-omics big-data integration techniques. (4) Better understanding of the multi-omics big-data mining techniques, as well as with different applications, for most insights from these omics data for TCM and disease researches. (5) TCM preparation quality control for checking both prescribed and unexpected ingredients including biological and chemical ingredients. (6) TCM preparation source tracking.  (7) TCM preparation network pharmacology analysis. (8) TCM analysis data resources, web services, and visualizations. (9) TCM geoherbalism examination and authentic TCM identification. Traditional Chinese Medicine has been in existence for several thousands of years, and only in recent tens of years have we realized that the researches on TCM could be profoundly boosted by the omics technologies. Devised as a book on TCM and disease researches in the omics age, this book has put the focus on data integration and data mining methods for multi-omics researches, which will be explained in detail and with supportive examples the "e;What"e;, "e;Why"e; and "e;How"e; of omics on TCM related researches. It is an attempt to bridge the gap between TCM related multi-omics big data, and the data-mining techniques, for best practice of contemporary bioinformatics and in-depth insights on the TCM related questions.

"This concise book for scientists and students interested in bioinformatics and data science covers all aspects of predictive modeling for biomarker discovery based on high-dimensional data, as well as modern data science methods for identification of parsimonious and robust multivariate biomarkers for medical diagnosis and personalized medicine"--

This second edition volume expands on the previous edition with discussions of the latest advancements and methods used by scientists to study systems biology. The chapters in this book are organized into four parts. Part One looks at models in systems biology and parameters identification such as short peptide analysis, metastasis models, and metabolomics. Part Two covers computational methods in the study of organisms, and cancer non-linear dynamics. Part Three discusses critical transition states across Waddington¿s like landscapes such as understanding cell differentiation through single-cell approaches and modeling mammary organogenesis from biological first principles. Part Four talks about specific fields of investigation including inborn errors of metabolism, system biology approach in epithelial-mesenchymal transition, and an approach to understanding how COVID-19 spreads in the population. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting-edge and comprehensive, Systems Biology, Second Edition is a valuable tool for any researcher looking to learn more about this important and developing field.

Different authors have addressed, for centuries, the use of the healing and spiritual properties of plants and minerals, but these had never been integrated into the basic principles of dowsing and radionics, so this work presents the union of this knowledge. This allows the use of these energies at a distance, in a simple, safe and effective way. Radionic Herbalism as a technique responds to the need to generate distance healing strategies, in view of the new world reality.

This book offers the reader a journey through the counterintuitive nature of Brownian motion under confinement. Diffusion is a universal phenomenon that controls a wide range of physical, chemical, and biological processes. The transport of spatially-constrained molecules and small particles is ubiquitous in nature and technology and plays an essential role in different processes. Understanding the physics of diffusion under conditions of confinement is essential for a number of biological phenomena and potential technological applications in micro- and nanofluidics, among others. Studies on diffusion under confinement are typically difficult to understand for young scientists and students because of the extensive background on diffusion processes, physics, and mathematics that is required. All of this information is provided in this book, which is essentially self-contained as a result of the authors¿ efforts to make it accessible to an audience of students from avariety of different backgrounds. The book also provides the necessary mathematical details so students can follow the technical process required to solve each problem. Readers will also find detailed explanations of the main results based on the last 30 years of research devoted to studying diffusion under confinement. The authors approach the physical problem from various angles and discuss the role of geometries and boundary conditions in diffusion. This textbook serves as a comprehensive and modern overview of Brownian motion under confinement and is intended for young scientists, graduate students, and advanced undergraduates in physics, physical chemistry, biology, chemistry, chemical engineering, biochemistry, bioengineering, and polymer and material sciences.

This book constitutes the refereed proceedings of the 21st International Conference on Computational Methods in Systems Biology, CMSB 2023, held in Luxembourg City, Luxembourg, during September 13¿15, 2023.The 14 full papers and 3 tool papers presented in this book were carefully reviewed and selected from 28 submissions. CMSB focuses on modeling, simulation, analysis, design and control of biological systems and covers the broad field of computational methods and tools in systems and synthetic biology and their applications.

This book reviews the advances in data gathering and processing in the biotech laboratory environment, and it sheds new lights on the various aspects that are necessary for the implementation of intelligent laboratory architecture and infrastructure. Smart technologies are increasingly dominating our everyday lives and have become an indispensable part of the industrial environment. The laboratory environment, which has long been rather conservative, has also set out to adapt smart technologies with regards to Industry 4.0 and the Internet of Things (IoT) for the laboratory. Due to the heterogeneity of the existing infrastructure and the often complex work processes, standardization is slow, e.g. to implement device interfaces or standardized driver protocols, which are urgently needed to generate standardized data streams that would be immanent for post-processing of data.Divided into 9 chapters, this book offers an authoritative overview of the diverse aspects in the generation and recording of uniform data sets in the laboratory, and in the processing of the data and enabling seamless processing towards machine learning and artificial intelligence. In the first part of the book, readers will find more about high throughout systems, automation, robotics, and the evolution of technology in the laboratory. The second part of the book is devoted to standardization in lab automation, in which readers will learn more about some regulatory aspects, the SiLA2 standards, the OPC LADS (Laboratory and Analytical Device Standard), and FAIR Data infrastructure

The three-dimensional structure and function of molecules present many challenges and opportunities for developing an understanding of biological systems. With the increasing availability of molecular structures and the advancing accuracy of structure predictions and molecular simulations, the space for algorithmic advancement on many analytical and predictive problems is both broad and deep. To support this field, a rich set of methods and algorithms are available, addressing a variety of important problems such as protein-protein interactions, the effect of mutations on protein structure and function, and protein structure determination. Despite recent advancements in the field, in particular in protein folding with the development of AlphaFold, many problems still remain unsolved.In this book we focus on a number of topics in Structural Bioinformatics: Cryo-EM structural detection, protein conformational exploration, elucidation of molecular binding surface using geometry, the effect of mutations, insertions and deletions on protein structural stability, and protein-ligand binding.

To date, processing of high-throughput Mass Spectrometry (MS) data is accomplished using serial algorithms. Developing new methods to process MS data is an active area of research but there is no single strategy that focuses on scalability of MS based methods.  Mass spectrometry is a diverse and versatile technology for high-throughput functional characterization of proteins, small molecules and metabolites in complex biological mixtures. In the recent years the technology has rapidly evolved and is now capable of generating increasingly large (multiple tera-bytes per experiment) and complex (multiple species/microbiome/high-dimensional) data sets. This rapid advance in MS instrumentation  must  be matched by equally fast and rapid evolution of scalable methods developed for analysis of these complex data sets. Ideally, the new methods should leverage the rich heterogeneous computational resources available in a ubiquitous fashion in the form of  multicore,  manycore,  CPU-GPU, CPU-FPGA, and IntelPhi architectures.  The absence of these high-performance computing algorithms now hinders scientific advancements for mass spectrometry research. In this book we illustrate the need for high-performance computing algorithms for MS based proteomics, and proteogenomics and showcase our progress in developing these high-performance algorithms.

The current study entitled ¿Characterization of induced mutants for earliness and anthracnose resistance traits of Common bean (Phaseolus vulgaris L.),¿ was carried out at Regional Horticulture Research Station, Bhaderwah, SKUAST-J during Kharif 2020 to assess the nature and magnitude of genetic variability, association, and diversity among 24 rajmash genotypes. Data on traits viz., plant height, days to flowering, days to maturity, number of seeds / pods, number of pods /plants, pod length, number of clusters per plant, 1000 seed weight, grain yield per plant, seed colour, anthracnose resistance, protein content, iron content, and zinc content were recorded. The mean data of all the characters under study were subjected to statistical analysis and the following conclusions were drawn: The analysis of variance revealed that all of the characteristics under consideration had extremely significant differences. This showed a high level of genetic variability for these traits.

This book presents contributions from the MICCAI 2022 Computational Biomechanics for Medicine Workshop. "Computational Biomechanics for Medicine - towards translation and better patient outcomes¿ comprises papers accepted for the MICCAI Computational Biomechanics for Medicine Workshop held in 2022 in Singapore. The content focuses on applications of computational biomechanics to computer-integrated medicine, which includes MICCAI topics of Medical Image Computing, Computer-Aided Modeling and Evaluation of Surgical Procedures, and Imaging, Analysis Methods for Image Guided Therapies, Computational Physiology, and Medical Robotics. Specific topics covered include medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, analysis of injury mechanisms, implant and prostheses design, as well as artificial organ design and medical robotics. This book details state-of-the-art progress in the above fields to researchers, students, and professionals.

This book presents novel statistics methods and reproducible software that helps to solve challenging problems in biomedicine. Specifically, it consists of a collection of 11 chapters contributed by some of the leading experts in the mathematical and statistical field which address new challenges in very disparate biomedical areas, such as genomics, cancer, circadian biology, microbiome, mental disorders, and more. The mathematical rigor is written in a user-friendly way to serve a general biomedical audience ranging from trainees or students to doctors, as well as scientific researchers, university departments, and PhD students.

This volume presents an array of different case studies which take as primary material data sourced from the NOW (¿New and Old Worlds¿) database of fossil mammals. The NOW database was one of the very first large paleobiological databases, and since 1996 it has been expanded from including mainly Neogene European land mammals to cover the entire Cenozoic at a global scale. In the last two decades the number of works that are based in the use of huge databases to explore ecological and evolutionary questions has increased exponentially, and even though the importance of big data in paleobiological research has been outlined in selected chapters of general works, no volume has appeared before this one which solely focuses on the databases as a primary source in reconstructing the past. The purpose of this book is to provide an illustrative volume showing the importance of big data in paleobiological research, and presenting a broad array of unpublished examples and case studies. The book is mainly aimed to professional palaeobiologists working with Cenozoic land mammals, but the scope of the book is broad enough to fit the interest for evolutionary biologists, paleoclimatologists and paleoecologists.The volume is divided in four parts. The first part includes two chapters on the development of large paleobiological databases, providing a first-hand account on the logic and the functioning of these databases. This is a much-needed perspective which is ignored by most researchers and users of such databases and, even if centered in the NOW database, the lessons that can be learned from this part can be extended to other examples. After this introductory part, the body of the book follows and is divided into three parts: patterns in regional faunas; large scale patterns and processes; and ecological, biogeographical and evolutionary patterns of key taxa. Each chapter is written by well-known specialists in the field, withsome participation of members of the NOW advisory board. The array of selected mammal taxa ranges from carnivores, equids, ruminants and rodents to the genus Homo. The topics studied also include the diversification and radiation of major clades, large-scale paleobiogeographical patterns, the evolution of ecomorphological patterns and paleobiological problems such as evolution of body size or species longevity. In most cases the results are discussed in relation to protracted environmental or paleogeographic changes.

This book gathers outstanding research papers presented at the 2nd International Conference on Frontiers in Computing and Systems (COMSYS 2021), organized by Department of Electronics and Communication Engineering and Department of Information Technology, North-Eastern Hill University, Shillong, Meghalaya, India held during September 29-October 1, 2021. The book presents the latest research and results in various fields of machine learning, computational intelligence, VLSI, networks and systems, computational biology, and security, making it a rich source of reference material for academia and industry alike.

This book gathers selected, extended and revised contributions to the 17th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and the 5th Conference on Imaging and Visualization (CMBBE 2021), held online on September 7-9, 2021, from Bonn, Germany. It reports on cutting-edge models, algorithms and imaging techniques for studying cells, tissues and organs in normal and pathological conditions. It covers numerical and machine learning methods, finite element modeling and virtual reality techniques, applied to understand biomechanics of movement, fluid and soft tissue biomechanics. It also reports on related advances in rehabilitation, surgery and diagnosis. All in all, this book offers a timely snapshot of the latest research and current challenges at the interface between biomedical engineering, computational biomechanics and biological imaging. Thus, it is expected to provide a source of inspiration for future research and cross-disciplinary collaborations.